Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008826.1 Corchorus capsularis cultivar CVL-1 contig08847, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53520
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:10606 original size:15 final size:15
Alignment explanation
Indices: 10586--10617 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10576 CAGAATATAG
10586 TTTGTAAGATAGAGC
1 TTTGTAAGATAGAGC
10601 TTTGTAAGATAGAGC
1 TTTGTAAGATAGAGC
10616 TT
1 TT
10618 CAACTAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (15 bp):
TTTGTAAGATAGAGC
Found at i:18263 original size:21 final size:21
Alignment explanation
Indices: 18221--18270 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
18211 GTTTATTAAG
18221 TATTAATTTAATAATATGA-TT
1 TATTAA-TTAATAATATGATTT
* *
18242 TATTAATTACTAATTATTATTT
1 TATTAATTAATAA-TATGATTT
18264 TATTAAT
1 TATTAAT
18271 AATTTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 10 0.40
22 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTAATTAATAATATGATTT
Found at i:21089 original size:18 final size:18
Alignment explanation
Indices: 21066--21126 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
21056 CATATTTTTC
21066 AATTAATTTTGTATCTAA
1 AATTAATTTTGTATCTAA
* * * * **
21084 AATTAAAATATATTTCTTC
1 AATT-AATTTTGTATCTAA
21103 AATTAATTTTGTATCTAA
1 AATTAATTTTGTATCTAA
21121 AATTAA
1 AATTAA
21127 AATCTATTTC
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (18 bp):
AATTAATTTTGTATCTAA
Found at i:21106 original size:37 final size:37
Alignment explanation
Indices: 21057--21136 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
21047 GACACATACC
21057 ATATTT-TTCAATTAATTTTGTATCTAAAATTAAAAT
1 ATATTTCTTCAATTAATTTTGTATCTAAAATTAAAAT
21093 ATATTTCTTCAATTAATTTTGTATCTAAAATTAAAAT
1 ATATTTCTTCAATTAATTTTGTATCTAAAATTAAAAT
*
21130 CTATTTC
1 ATATTTC
21137 CTAAAAGACA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 6 0.14
37 36 0.86
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.50
Consensus pattern (37 bp):
ATATTTCTTCAATTAATTTTGTATCTAAAATTAAAAT
Found at i:23520 original size:33 final size:33
Alignment explanation
Indices: 23482--23561 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
23472 AGCACTTGTG
*
23482 ACCGGCCACGCGACTTGGAGATGTCCGACCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
* *
23515 ACCGGCCACGCGACTTGGAGTTGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC
23548 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
23562 AAGGACATGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.19, C:0.40, G:0.29, T:0.12
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGACCATC
Found at i:23578 original size:33 final size:32
Alignment explanation
Indices: 23482--23588 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
23472 AGCACTTGTG
*
23482 ACCGGCCACGCGACTTGGAGATGTCCGACCATC
1 ACCGGCCACGCGACTTGGAGATG-CCGGCCATC
*
23515 ACCGGCCACGCGACTTGGAGTTGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATG-CCGGCCATC
** *
23548 ACCGGCCACGCGACAAGGACATGCCTGGCCA-C
1 ACCGGCCACGCGACTTGGAGATGCC-GGCCATC
23580 AACCGGCCA
1 -ACCGGCCA
23589 AATGAATCGG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 3 0.05
33 62 0.95
ACGTcount: A:0.21, C:0.39, G:0.28, T:0.11
Consensus pattern (32 bp):
ACCGGCCACGCGACTTGGAGATGCCGGCCATC
Found at i:30061 original size:33 final size:33
Alignment explanation
Indices: 30023--30097 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
30013 AGCACTTGTG
*
30023 ACCGGCCACGCGACTTGGAGATGTCCGACCA-TC
1 ACCGGCCACGCGACTTGGAGATG-CCCACCATTC
* *
30056 ACCGGCCACGCGACTTGGAGTTGCCCAGCATTC
1 ACCGGCCACGCGACTTGGAGATGCCCACCATTC
30089 ACCGGCCAC
1 ACCGGCCAC
30098 AACCGGCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.15
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCACCATTC
Found at i:50117 original size:8 final size:8
Alignment explanation
Indices: 50104--50139 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
50094 TCTTGCGGTG
50104 TTTTAATT
1 TTTTAATT
50112 TTTTAATT
1 TTTTAATT
50120 TTTTAATT
1 TTTTAATT
50128 TTTTAATT
1 TTTTAATT
50136 TTTT
1 TTTT
50140 TTTTCGTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTAATT
Found at i:51822 original size:23 final size:24
Alignment explanation
Indices: 51796--51845 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
51786 ATACGCCCTA
51796 AAAAAT-AAGGTACCAAATACTCG
1 AAAAATCAAGGTACCAAATACTCG
51819 AAAAATCAAGGTACCAAATACTCG
1 AAAAATCAAGGTACCAAATACTCG
51843 AAA
1 AAA
51846 GTTTTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAAATCAAGGTACCAAATACTCG
Found at i:53395 original size:43 final size:43
Alignment explanation
Indices: 53311--53396 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
53301 ATACACAACA
* *
53311 TTATTTGATGACTATAATGAGATTGTTCAGGTGATCGAGTGTT
1 TTATTTGATGACTATAATGAGATTGGTCAGGTGATCAAGTGTT
* * * *
53354 TTATTTGATGATTGTAATGAGATTGGTCTGGTGATTAAGTGTT
1 TTATTTGATGACTATAATGAGATTGGTCAGGTGATCAAGTGTT
53397 GAATTCTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44
Consensus pattern (43 bp):
TTATTTGATGACTATAATGAGATTGGTCAGGTGATCAAGTGTT
Done.